January 30, 2012

AAPA 2012 abstracts (Part 2)

I am quite looking forward to the following study which echoes some of my own thoughts on the subject:

Vindija Neandertals as evidence for gene flow from early modern humans.
FRED H. SMITH and ARIKA M. WARD.

The Vindija Neandertal remains have played a critical role in discussions on the emergence of modern Eurasians and the possible involvement of Neandertals in that process. Most recently, fragments from Vindija yielded a draft sequence of a Neandertal genome revealing a 1-4% contribution of Neandertals to recent Eurasians. Morphology of the Vindija Neandertals has long been regarded as showing progressive features in a late Neandertal sample, but the interpretation of the meaning of this pattern has varied over time. Although various studies have shown the Vindija pattern is not due to any type of sample bias, that interpretation is still cited. Otherwise the morphology is seen as either reflecting the process of modern human emergence in Eurasia or as just a part of “normal” Neandertal variation. If Vindija does reflect the process of transition to modern humans, the question is how does it reflect this process? We suggest that the Vindija morphology reflects evidence for gene flow from early modern populations into Neandertals. We show how the Vindija cranial and mandibular pattern reflects that process and demonstrate that indications of mixing among stratigraphic levelsat the site do not impact biological interpretations of the Vindija sample. This direction of gene flow has not been detected in genetic studies so far. Our interpretation underscores the importance of using both morphological and genetic data in approaching questions of late human evolution.

Assessing the pattern of Neandertal ancestry in living human populations.
JOHN HAWKS. Department of Anthropology, University of Wisconsin-Madison.

People living outside Africa today derive 2 to 4% of their ancestry from Neandertal populations. This initial estimate was based on whole-genome sequencing of a small number of individuals, and the pattern of Neandertal ancestry has yet to be characterized. Here I employ the sequencing data from the 1000 Genomes Project to identify Neandertal-derived haplotypes in living human populations. Initial sequence-level comparison allowed development of a genome-wide sample of SNP haplotypes informative of Neandertal ancestry. Humans within a population differ little in the amount of Neandertal ancestry, but the fraction does vary significantly among samples from different regions. Most Neandertal genes today are rare, existing only in one or two copies in the 1000 Genomes sample. However, a few have become majority haplotypes, 50% or higher. Europeans, South Asians, and East Asian populations differ substantially in which Neandertal-derived haplotypes are presently common, so that a haplotype present in one of these regions is very likely to be absent in samples from other regions. This heterogeneity of present-day Neandertal ancestry provides information about the Late Pleistocene dispersals of humans. In particular, today's populations outside Africa differentiated under strong genetic drift. A relatively small proportion of Neandertal-derived haplotypes contain candidates for selection in later human populations, based on their current pattern of extended haplotype heterozygosity and fraction of derived SNP alleles. Additionally, I report on the application of these methods to investigate and visualize Neandertal ancestry at the whole-genome level from commercial SNP genotype data.

The Neandertal genome project recently estimated that 1-4% of the genetic material found in non-African populations is the result of the introgression of Neandertal genes. When populations that were previously isolated admix, incompatibility at the genic level can often result in distinctive patterns of introgression. It can be predicted that intergenic regions will be more likely to introgress into a population than protein coding changes when two populations or species have lowered hybrid viability or fertility. As coding changes are more likely to be associated with inviability and infertility due to epistatic interactions between gene products, these regions are less likely to be exchanged between diverging populations. Coding regions, therefore, should show an earlier divergence time than intergenic regions. To test this hypothesis, we looked at Neandertal introgression in five genic and five intergenic regions from six geographically distinct modern human populations (Han Chinese, Gujarati Indian, Italian, Puerto Rican, Japanese, and CEPH Europeans). We chose regions with similar recombination rates that did not show strong departures from neutrality. Using maximum likelihood estimation, we calculated the time to the most recent common ancestor (TMRCA) for each of the 10 regions separately based on human-Neanderthal-chimp sequence alignments. Our results highlight the patterns of introgression for intergenic and coding regions in different human populations while expanding our understanding of Neandertal population dynamics and raising new questions about human-Neandertal admixture.

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